1. Field of the Invention
This invention relates generally to screening for risk or or presence of neoplastic disorders, and more particularly to screening for biomarkers present in a biological sample obtained from a subject that are indicative of a predisposition for a neoplastic (e.g., benign or malignant) or cell proliferative disorder.
2. Background Information
Each mammalian cell carries two copies of each gene, one inherited from the mother (on the maternal chromosome) and one inherited from the father (on the paternal chromosome). Most of the autosomal genes and X-linked genes in females are therefore biallelic i.e. both paternal and maternal alleles of the gene are expressed and the information of both copies is actively used in protein synthesis. However, in humans and other mammals, monoallelic expression of biallelic genes has been demonstrated. Allelic exclusion can result from two different mechanisms. The first mechanism is independent of the parental origin. The second mechanism, called genomic imprinting, is an epigenetic modification of a specific parental chromosome in the gamete or zygote that leads to monoallelic or differential expression of the two alleles of a gene in somatic cells of the offspring. Imprinting affects various essential cellular and developmental processes, including intercellular signaling, RNA processing, cell cycle control, and promotion or inhibition of cellular division and growth.
Imprinted genes can show monoallelic expression in some tissues and biallelic expression in others. For example, the insulin-like growth factor II gene (IGF2) is imprinted in most tissues but is biallelic in brain and monoallelically expressed in liver. Loss of imprinting (LOI) of the IGF2 gene, or activation of the normally silent maternally inherited allele, occurs in many common cancers (Feinberg, A., Semin. Cancer Biol. 14, 427 (2004)). The term LOI simply means loss of preferential parental origin-specific gene expression and can involve either abnormal expression of the normally silent allele, leading to biallelic expression, or silencing of the normally expressed allele, leading to epigenetic silencing of the locus. About 10% of the population shows LOI of IGF2, and this molecular trait is associated with a personal and/or family history of colorectal neoplasia (Cui et al., Science 299, 1753 (2003); Woodson et al., J. Natl. Cancer. Inst. 96, 407 (2004)). Imprinting of IGF2 is regulated by a differentially methylated region (DMR) upstream of the nearby untranslated H19 gene. Deletion of the DMR leads to biallelic expression (LOI) of IGF2 in the offspring when the deletion is maternally inherited (Leighton, et al., Nature 375, 34 (1995); Ripoche, et al., Genes Dev. 11, 1596 (1997)). Thus, abnormal imprinting in cancer can lead to activation of normally silent alleles of growth-promoting genes.
Currently, no single biochemical marker, or plurality of biochemical markers, reliably identifies a subject at risk for developing a disease associated with LOI and/or uncontrolled cell proliferation or neoplastic disorders (e.g., benign and cancer). Thus, there exists a need for diagnostic methods and compositions that can utilize cell differentiation information to identify those individuals at risk for developing a cell proliferation or neoplastic disorder. Such information can optionally be correlated with abnormal gene expression resulting from epigenetic alterations in the genome of a subject. Early implementation of a prophylactic therapy and periodic screening can lead to prevention of such a disorder.